This study retrospectively evaluated the effectiveness of pulmonary vasodilator therapy with bosentan (n = 14) and/ or sildenafil (n = 23) in 34 patients with a functionally single ventricle. Vasodilator therapy was initiated before the Fontan procedure in 18 patients and after the procedure in 16 patients. The reasons for vasodilator treatment included high pulmonary artery pressure or pulmonary vascular resistance (n = 8), high central venous pressure after the Fontan or bidirectional Glenn procedure (n = 7), and ventilatory impairment (n = 8). In the 11 patients who underwent right heart catheterization before and after the initiation of therapy, the mean pulmonary artery pressure decreased significantly from 19.5 ± 5.5 mmHg to 14.3 ± 3.0 mmHg (P = 0.023) and the transpulmonary pressure gradient decreased significantly from 10.9 ± 4.6 mmHg to 7.2 ± 3.3 mmHg (P = 0.046). Of the 18 patients who started vasodilator therapy before the Fontan procedure, 10 survived surgery, 4 are awaiting surgery, 3 had not been evaluated for the Fontan procedure at the end of the study period, and 1 died of heart failure after discontinuing bosentan therapy. There were no deaths among the patients who started therapy after the Fontan procedure. Two of the 14 patients receiving bosentan discontinued treatment because of adverse effects (hepatic dysfunction and increased serum brain natriuretic peptide level). Bosentan or sildenafil therapy is usually safe and may contribute to reducing pulmonary vascular resistance in patients with a functionally single ventricle before and after a Fontan type operation.